[Insight-users] Itk Segmentation Filter for nuclei

[Bradley Lowekamp]

Hello,

The images you provided are black and white shouldn't H&E stained image be color? You may tried using VectorConfidenceConnetedImageFilter, on the color image either with a single seed or in groups to estimate the global color range of the nuclei. You should also consider the color space used, and if it would be best to do the range in a perceptual based space, or not.

If the segmentation is predictable under-segmented by a certain number pixels around the boarder you may consider just refining the segmentation with a geodesic dilation of an over-segmentation.

Just a couple of suggestions to help you explore algorithms to try to find a solution to your problem.

Brad

On May 3, 2012, at 5:46 AM, Humayun Irshad wrote:

> ITK Experts,
> 
> I need to segment nuclei (specially mitosis nuclei) in H&E stained histopathological images (see in attachment). I have seed points. I tried ConfidenceConnectedImageFilter and FastMarchingImageFilter but it give poor results. Most of the time, nuclei are under segment. Mitosis nuclei are homogeneous and having variations in shape and size. Please suggest any better segmentation filter. 
> 
> -- 
> -- 
> Best Regards, 
> 
> HUMAYUN IRSHAD
> PhD student, University of Joseph Fourier, Grenoble, France
> Research Engineer,  IPAL – Image & Pervasive Access Lab, Singapore
> UMI CNRS (I2R/A*STAR, NUS, UJF, UPMC, IT)
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========================================================
Bradley Lowekamp  
Medical Science and Computing for
Office of High Performance Computing and Communications
National Library of Medicine 
blowekamp at mail.nih.gov



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